Recently Sony submitted it’s Reader app to Apple to bring Sony Reader to the iOS platform. Unfortunately for Sony, Apple rejected the app. Unfortunately for iOS users, the reason why could easily be an issue for Amazon Kindle, Barnes & Noble Nook, Kobo, or any other company that offers eBooks through iOS apps.

According to Trudy Miller, an Apple spokesperson who talked to All Things D, Apple is “now requiring that if an app offers customers the ability to purchase books outside of the app, that the same option is also available to customers from within the app with in-app purchase.” Technically this isn’t a change from the App Store Guidelines, but it is a different way of enforcing them. According to the guidelines, an app that allows for paid content must offer the option to offer that content through Apple’s payment API. So, Sony can’t direct Reader users to Mobile Safari to read books in the Reader app, it also needs to offer those books through Apple’s API, which would give Apple a 30-percent cut of the payment.

That means that the Kindle, Nook and Kobo apps that are currently available through the App Store wouldn’t be accepted if they were submitted today since none offer users to buy eBooks through the app. Sure, it could be easier to buy those eBooks through the apps, but how would that effect the price of eBooks if Amazon, Sony, Barnes & Noble, and Kobo don’t want to give a straight 30-percent cut to Apple. In-app purchases are also regulated by Apple, just ask Comixology who routinely sees sales end early when buying through the iOS app because Apple changes the prices earlier than the company’s website does.

If Apple intends to follow through with this in all eBooks apps, or other apps that link to paid services, it raises a lot of questions. Would Pandora have to add an option to buy a subscription through it’s iOS app? What about Dropbox, Netflix, or Hulu? We’ll just have to wait and see what comes out of it, hopefully it doesn’t change anythign for the worse.